bug fix: check bp char to int

Al-Murphy · Jul 20, 2023 · 5ad4a42 · 5ad4a42
1 parent 7f292ca
commit 5ad4a42
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: MungeSumstats
 Type: Package
 Title: Standardise summary statistics from GWAS
-Version: 1.9.12
+Version: 1.9.13
 Authors@R:
     c(person(given = "Alan",
            family = "Murphy",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+## CHANGES IN VERSION 1.9.13
+
+### Bug fix
+* In `check_bp_range` ensure that the BP column is numeric.
+
 ## CHANGES IN VERSION 1.9.12
 
 ### Bug fix

diff --git a/R/check_bp_range.R b/R/check_bp_range.R
@@ -27,10 +27,15 @@ check_bp_range <- function(sumstats_dt, path, ref_genome,log_folder_ind,
         genome_info <-
           cbind(data.table::data.table("CHR"=seqnames(genome_info)),
                 data.table::as.data.table(genome_info))
-        #convwert CHR to char in sumstats (if it is an int)
+        #convert CHR to char in sumstats (if it is an int)
         sumstats_dt[,CHR:=as.character(CHR)]
         #add chr len to sumstats
         sumstats_dt[genome_info,chr_max:=seqlengths,on="CHR"]
+        #ensure BP numeric
+        if(!is.integer(sumstats_dt$BP)){
+          message("Coercing BP column to numeric.")
+          sumstats_dt[,BP:=as.numeric(BP)]
+        }  
         #now check if BP value is too large/less than 0
         #s.na(chr_max) in case chr formatting not found
         bad_bp <- sumstats_dt[!is.na(chr_max) & (is.na(BP)|BP<=0 |BP>chr_max),]